Intersting question. I just picked up a copy of ‘Food for Fitness‘ by Chris Carmichael and he specifically address' the benefit of cycling vs. running in improving aerobic conditioning and recommends it to athelete's from other sports over running. He states that cycling can improve aerobic condition better than running in part because one can stay in the optimum heart rate zone easier and longer than running. He also says that running places a greater stress on the anerobic system, which burns fuel differently.
I'll be interested in hearing how things go for you and what you perceive the benefits are of riding vs running.